rs2740566

Variant names:

• chr7-99817782-G-A
• rs2740566

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.789 in 152,138 control chromosomes in the GnomAD database, including 53,031 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (53031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119945 AN: 152020 Hom.: 53028 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.836

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.789 AC: 119971 AN: 152138 Hom.: 53031 Cov.: 31 AF XY: 0.796 AC XY: 59162 AN XY: 74354

African (AFR) AF: 0.348 AC: 14442 AN: 41446

American (AMR) AF: 0.886 AC: 13538 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3312 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5146 AN: 5156

South Asian (SAS) AF: 0.980 AC: 4727 AN: 4824

European-Finnish (FIN) AF: 0.964 AC: 10224 AN: 10608

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65720 AN: 68028

Other (OTH) AF: 0.836 AC: 1763 AN: 2110

Alfa AF: 0.776 Hom.: 9816

Bravo AF: 0.762

Asia WGS AF: 0.943 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.70
PhyloP100		-2.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2740566; hg19: chr7-99415405;